Nucleic acid and amino acid sequences relating to Bacteroides fragilis for diagnostics and therapeutics

• US 20060073161A1
• Filed: 03/14/2005
• Published: 04/06/2006
• Est. Priority Date: 04/09/1999
• Status: Abandoned Application

• Current Assignee: Genome Therapeutics Corporation
• Original Assignee: Genome Therapeutics Corporation
• Inventors: Breton, Gary L.
• Application Number:
  US11/079,463
• Publication Number:
  US 20060073161A1
• Time in Patent Office: Days
• US Class Current: 424/190.100
• CPC Class Codes: A61K 39/00 Medicinal preparations containing antigens or antibodies materials for immunoassay G01N33/53
• CPC Class Codes: C07K 14/195 from bacteria
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: Y10S 977/924 using nanostructure as support of dna analysis

Abstract

The invention provides isolated polypeptide and nucleic acid sequences derived from Bacteroides fragilis that are useful in diagnosis and therapy of pathological conditions; antibodies against the polypeptides; and methods for the production of the polypeptides. The invention also provides methods for the detection, prevention and treatment of pathological conditions resulting from bacterial infection.

Claims

1. An isolated nucleic acid encoding an B. fragilis polypeptide of SEQ ID NOS:

5223-10444.

2. A recombinant expression vector comprising the nucleic acid of claim 1 operably linked to a transcription regulatory element.

3. A cell comprising a recombinant expression vector of claim 2.

4. A method for producing an B. fragilis polypeptide comprising culturing a cell of claim 3 under conditions that permit expression of the polypeptide.

5. An isolated nucleic acid selected from the group consisting of:

(a) SEQ ID NOS;

1-5222;

(b) a complement of SEQ ID NOS;

1-5222;

or

(c) an RNA of (a) or (b), wherein U is substituted for T.

6. A recombinant expression vector comprising the nucleic acid of claim 5 operably linked to a transcription regulatory element.

7. A cell comprising a recombinant expression vector of claim 6.

8. A method for producing an B. fragilis polypeptide comprising culturing a cell of claim 7 under conditions that permit expression of the polypeptide.

11. A vaccine composition for prevention or treatment of an B. fragilis infection comprising a nucleic acid of claim 5 and a pharmaceutically acceptable carrier.

12. A vaccine composition of claim 11, further comprising an adjuvant.

13. A vaccine composition of claim 11, further comprising one or more additional ingredients.

14. A method of treating a subject for B. fragilis infection comprising administering to a subject a vaccine composition of claim 11, such that treatment of B. fragilis infection occurs.

15. A method of claim 14, wherein the treatment is a prophylactic treatment.

16. A method of claim 14, wherein the treatment is a therapeutic treatment.

24. A method for detecting the presence or absence of a Bacteroides nucleic acid in a sample comprising:

(a) contacting a sample with the nucleic acid of claim 5 under conditions in which a hybrid can form between a probe comprising a nucleotide sequence consisting of at least eight contiguous nucleotides of a nucleotide sequence selected from the group consisting of SEQ ID NOS;

1-5222 or a complement of SEQ ID NOS;

1-5222 and a Bacteroides nucleic acid in the sample; and

(b) detecting the hybrid formed in step (a), wherein detection of a hybrid indicates the presence or absence of a Bacteroides nucleic acid in the sample.

9. A probe comprising a nucleotide sequence consisting of at least eight contiguous nucleotides of a nucleotide sequence selected from the group consisting of:

(a) SEQ ID NOS;

1-5222;

(b) a complement of SEQ ID NOS;

1-5222;

or

(c) an RNA of (a) or (b), wherein U is substituted for T.

10. An isolated nucleic acid comprising a nucleotide sequence of at least eight nucleotides in length, wherein the sequence is hybridizable to a nucleic acid having a nucleotide sequence selected from the group consisting of:

(a) SEQ ID NOS;

1-5222;

(b) a complement of SEQ ID NOS;

1-5222;

or

(c) an RNA of (a) or (b), wherein U is substituted for T.

17. A recombinant or substantially pure preparation of an B. fragilis polypeptide or a fragment thereof, wherein said B. fragilis polypeptide is SEQ ID NOS:

5223-10444.

18. A vaccine composition for prevention or treatment of an B. fragilis infection comprising an B. fragilis polypeptide of claim 17 and a pharmaceutically acceptable carrier.

19. A vaccine composition of claim 18, further comprising an adjuvant.

20. A vaccine composition of claim 18, further comprising one or more additional ingredients.

21. A method of treating a subject for B. fragilis infection comprising administering to a subject a vaccine composition of claim 18, such that treatment of B. fragilis infection occurs.

22. A method of claim 21, wherein the treatment is a prophylactic treatment.

23. A method of claim 21, wherein the treatment is a therapeutic treatment.

25. A computer readable medium having recorded thereon a nucleotide sequence selected from the group consisting of:

(a) SEQ ID NOS;

1-5222;

(b) a complement of SEQ ID NOS;

1-5222;

(c) an RNA of (a) or (b), wherein U is substituted for T;

or

(d) a fragment of (a), (b) or (c).

26. A computer based system for identifying fragments of the Bacteroides genome of comprising;

a) a data storage means comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS;

1-5222, a complement of SEQ ID NOS;

1-5222, or a fragment thereof,

b) a search means for comparing a target sequence to the nucleotide sequences of the data storage means of step (a) to identify homologous sequences, and;

c) a retrieval means for obtaining said homologous sequences(s) of step (b).

27. A method of identifying nucleic acid fragments of a Bacteroides genome comprising comparing a database comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS:

1-5222;

a complement of SEQ ID NOS;

1-5222;

or a fragment thereof with a target sequence to obtain a nucleic acid molecule comprised of a complementary nucleotide sequence to said target sequence, wherein said target sequence is not randomly selected.

28. A method for identifying an expression modulating fragment of the Bacteroides genome comprising comparing a database comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS:

1-5222;

a complement of SEQ ID NOS;

1-5222;

or fragment thereof with a target sequence to obtain a nucleic acid molecule comprised of a complementary nucleotide sequence to said target sequence, wherein said target sequence comprises sequences known to regulate gene expression.